Mercurial > repos > vandelj > giant_hierarchical_clustering
annotate src/VolcanoPlotsScript.R @ 0:14045c80a222 draft
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
author | vandelj |
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date | Fri, 26 Jun 2020 09:38:23 -0400 |
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rev | line source |
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0
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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1 # R script to plot volcanos through Galaxy based GIANT tool |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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2 # written by Jimmy Vandel |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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3 # |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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4 # |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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5 initial.options <- commandArgs(trailingOnly = FALSE) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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6 file.arg.name <- "--file=" |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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7 script.name <- sub(file.arg.name, "", initial.options[grep(file.arg.name, initial.options)]) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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8 script.basename <- dirname(script.name) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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9 source(file.path(script.basename, "utils.R")) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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10 source(file.path(script.basename, "getopt.R")) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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11 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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12 #addComment("Welcome R!") |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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13 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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14 # setup R error handling to go to stderr |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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15 options( show.error.messages=F, error = function () { cat(geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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16 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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17 # we need that to not crash galaxy with an UTF8 error on German LC settings. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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18 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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19 loc <- Sys.setlocale("LC_NUMERIC", "C") |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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20 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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21 #get starting time |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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22 start.time <- Sys.time() |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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23 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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24 options(stringAsfactors = FALSE, useFancyQuotes = FALSE) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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25 args <- commandArgs() |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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26 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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27 # get options, using the spec as defined by the enclosed list. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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28 # we read the options from the default: commandArgs(TRUE). |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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29 spec <- matrix(c( |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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30 "statisticsFile", "i", 1, "character", |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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31 "volcanoName" , "n", 1, "character", |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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32 "pvalColumnName" , "p", 1, "character", |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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33 "fdrColumnName" , "m", 1, "character", |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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34 "fcColumnName" , "c", 1, "character", |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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35 "fcKind","d", 1, "character", |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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36 "fdrThreshold","s", 1, "double", |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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37 "fcThreshold","e", 1, "double", |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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38 "organismID","x",1,"character", |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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39 "rowNameType","y",1,"character", |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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40 "log", "l", 1, "character", |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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41 "outputFile" , "o", 1, "character", |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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42 "format", "f", 1, "character", |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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43 "quiet", "q", 0, "logical"), |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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44 byrow=TRUE, ncol=4) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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45 opt <- getopt(spec) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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46 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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47 # enforce the following required arguments |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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48 if (is.null(opt$log)) { |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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49 addComment("[ERROR]'log file' is required\n") |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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50 q( "no", 1, F ) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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51 } |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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52 addComment("[INFO]Start of R script",T,opt$log,display=FALSE) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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53 if (is.null(opt$statisticsFile)) { |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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54 addComment("[ERROR]'statisticsFile' is required",T,opt$log) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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55 q( "no", 1, F ) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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56 } |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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57 if (length(opt$pvalColumnName)==0 || length(opt$fdrColumnName)==0 || length(opt$fcColumnName)==0) { |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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58 addComment("[ERROR]no selected columns",T,opt$log) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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59 q( "no", 1, F ) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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60 } |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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61 if (length(opt$pvalColumnName)!=length(opt$fcColumnName) || length(opt$pvalColumnName)!=length(opt$fdrColumnName)) { |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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62 addComment("[ERROR]different number of selected columns between p.val, adj-p.val and FC ",T,opt$log) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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63 q( "no", 1, F ) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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64 } |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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65 if (is.null(opt$fcKind)) { |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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66 addComment("[ERROR]'fcKind' is required",T,opt$log) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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67 q( "no", 1, F ) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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68 } |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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69 if (is.null(opt$fdrThreshold)) { |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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70 addComment("[ERROR]'FDR threshold' is required",T,opt$log) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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71 q( "no", 1, F ) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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72 } |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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73 if (is.null(opt$fcThreshold)) { |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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74 addComment("[ERROR]'FC threshold' is required",T,opt$log) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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75 q( "no", 1, F ) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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76 } |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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77 if (is.null(opt$outputFile)) { |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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78 addComment("[ERROR]'output file' is required",T,opt$log) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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79 q( "no", 1, F ) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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80 } |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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81 if (is.null(opt$format)) { |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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82 addComment("[ERROR]'output format' is required",T,opt$log) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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83 q( "no", 1, F ) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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84 } |
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85 |
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86 #demande si le script sera bavard |
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87 verbose <- if (is.null(opt$quiet)) { |
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88 TRUE |
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89 }else{ |
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90 FALSE |
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91 } |
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92 |
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93 #paramètres internes |
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94 addComment("[INFO]Parameters checked test mode !",T,opt$log,display=FALSE) |
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95 |
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96 addComment(c("[INFO]Working directory: ",getwd()),TRUE,opt$log,display=FALSE) |
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97 addComment(c("[INFO]Command line: ",args),TRUE,opt$log,display=FALSE) |
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98 |
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99 #directory for plots |
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100 dir.create(file.path(getwd(), "plotDir")) |
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101 dir.create(file.path(getwd(), "plotLyDir")) |
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102 |
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103 #charge des packages silencieusement |
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104 suppressPackageStartupMessages({ |
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105 library("methods") |
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106 library("biomaRt") |
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107 library("ggplot2") |
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108 library("plotly") |
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109 library("stringr") |
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110 }) |
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111 |
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112 #define some usefull variable |
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113 nbVolcanosToPlot=length(opt$pvalColumnName) |
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114 |
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115 #load input file |
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116 statDataMatrix=read.csv(file=file.path(getwd(), opt$statisticsFile),header=F,sep="\t",colClasses="character") |
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117 #remove first colum to convert it as rownames |
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118 rownames(statDataMatrix)=statDataMatrix[,1] |
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119 statDataMatrix=statDataMatrix[,-1] |
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120 |
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121 #identify lines without adjusted p-value info (should contain the same content as rownames) and replace them with NA values |
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122 FDRinfo=rep(TRUE,nbVolcanosToPlot) |
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123 for(iVolcano in 1:nbVolcanosToPlot){ |
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124 #input parameter should be None when adjusted p-val are not available |
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125 if(opt$fdrColumnName[iVolcano]=="None"){ |
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126 #content of the corresponding column should also be the same as rownames |
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127 if(!all(statDataMatrix[,(iVolcano-1)*3+2]==rownames(statDataMatrix))){ |
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128 addComment(c("[ERROR]It seems that input stat matrix contains adjusted p-values for volcano",iVolcano,"whereas input parameter indicates that not."),T,opt$log) |
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129 q( "no", 1, F ) |
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130 } |
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131 FDRinfo[iVolcano]=FALSE |
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132 statDataMatrix[,(iVolcano-1)*3+2]=NA |
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133 } |
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134 } |
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135 |
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136 if(is.data.frame(statDataMatrix)){ |
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137 statDataMatrix=data.matrix(statDataMatrix) |
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138 }else{ |
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139 statDataMatrix=data.matrix(as.numeric(statDataMatrix)) |
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140 } |
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141 |
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142 #check if available column number match with volcano requested number |
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143 if(ncol(statDataMatrix)!=3*nbVolcanosToPlot){ |
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144 addComment("[ERROR]Input file column number is different from requested volcano number",T,opt$log) |
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145 q( "no", 1, F ) |
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146 } |
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147 |
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148 #build global dataFrame with data and fill with p.val and log2(FC) and FDR |
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149 dataFrame=data.frame(row.names = rownames(statDataMatrix)) |
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150 #start with p-value |
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151 dataFrame$p.value=statDataMatrix[,seq(1,nbVolcanosToPlot*3,3),drop=FALSE] |
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152 #compute FDR if needed or just get available info |
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153 dataFrame$adj_p.value=dataFrame$p.value |
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154 for(iVolcano in 1:nbVolcanosToPlot){ |
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155 #adjusted p-value are already computed |
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156 if(FDRinfo[iVolcano]){ |
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157 dataFrame$adj_p.value[,iVolcano]=statDataMatrix[,(iVolcano-1)*3+2,drop=FALSE] |
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158 }else{ |
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159 #adjusted p-value should be computed based on p-val using FDR |
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160 dataFrame$adj_p.value[,iVolcano]=p.adjust(dataFrame$p.value[,iVolcano,drop=FALSE],"fdr") |
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161 addComment(c("[INFO]Adjusted p-values are not available in input for volcano",iVolcano,", FDR approach will be used on available raw p-values"),T,opt$log) |
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162 } |
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163 } |
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164 if(opt$fcKind=="FC"){ |
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165 #we should transform as Log2FC |
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166 dataFrame$coefficients=log2(statDataMatrix[,seq(3,nbVolcanosToPlot*3,3),drop=FALSE]) |
14045c80a222
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167 addComment(c("[INFO]FC are converted in log2(FC) for plotting"),T,opt$log) |
14045c80a222
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168 }else{ |
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169 dataFrame$coefficients=statDataMatrix[,seq(3,nbVolcanosToPlot*3,3),drop=FALSE] |
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170 } |
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171 |
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172 addComment(c("[INFO]Input data available for",nbVolcanosToPlot,"volcano(s) with",nrow(statDataMatrix),"rows"),T,opt$log) |
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173 |
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174 |
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175 #plot VOLCANOs |
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176 volcanoPerPage=1 |
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177 logFCthreshold=log2(opt$fcThreshold) |
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178 iToPlot=1 |
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179 plotVector=list() |
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180 volcanoNameList=c() |
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181 for (iVolcano in 1:nbVolcanosToPlot){ |
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182 |
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183 if(nchar(opt$volcanoName[iVolcano])>0){ |
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184 curentVolcanoName=opt$volcanoName[iVolcano] |
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185 }else{ |
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186 curentVolcanoName=paste(iVolcano,opt$pvalColumnName[iVolcano],sep="_") |
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187 } |
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188 |
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189 #keep only rows without NA for p-val, adjusted p-val and coeff |
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190 pValToPlot=dataFrame$p.value[,iVolcano] |
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191 fdrToPlot=dataFrame$adj_p.value[,iVolcano] |
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192 coeffToPlot=dataFrame$coefficients[,iVolcano] |
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193 |
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194 rowToRemove=unique(c(which(is.na(pValToPlot)),which(is.na(fdrToPlot)),which(is.na(coeffToPlot)))) |
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195 if(length(rowToRemove)>0){ |
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196 pValToPlot=pValToPlot[-rowToRemove] |
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197 fdrToPlot=fdrToPlot[-rowToRemove] |
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198 coeffToPlot=coeffToPlot[-rowToRemove] |
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199 } |
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200 addComment(c("[INFO]For",curentVolcanoName,"volcano,",length(rowToRemove),"rows are discarded due to NA values,",length(pValToPlot),"remaining rows."),T,opt$log) |
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201 |
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202 #save volcano name |
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203 volcanoNameList=c(volcanoNameList,curentVolcanoName) |
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204 |
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205 #remove characters possibly troubling |
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206 volcanoFileName=iVolcano |
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207 |
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208 #define the log10(p-val) threshold corresponding to FDR threshold fixed by user |
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209 probeWithLowFDR=-log10(pValToPlot[which(fdrToPlot<=opt$fdrThreshold)]) |
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210 pvalThresholdFDR=NULL |
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211 if(length(probeWithLowFDR)>0)pvalThresholdFDR=min(probeWithLowFDR) |
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212 |
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213 #get significant points over FC and FDR thresholds |
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214 significativePoints=intersect(which(abs(coeffToPlot)>=logFCthreshold),which(fdrToPlot<=opt$fdrThreshold)) |
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215 |
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216 #to reduce size of html plot, we keep 20000 points maximum sampled amongst genes with pval>=33%(pval) and abs(log2(FC))<=66%(abs(log2(FC))) |
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217 htmlPointsToRemove=intersect(which(abs(coeffToPlot)<=quantile(abs(coeffToPlot),c(0.66))),which(pValToPlot>=quantile(abs(pValToPlot),c(0.33)))) |
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218 if(length(htmlPointsToRemove)>20000){ |
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219 htmlPointsToRemove=setdiff(htmlPointsToRemove,sample(htmlPointsToRemove,20000)) |
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220 }else{ |
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221 htmlPointsToRemove=c() |
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222 } |
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223 |
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224 xMinLimPlot=min(coeffToPlot)-0.2 |
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225 xMaxLimPlot=max(coeffToPlot)+0.2 |
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226 yMaxLimPlot= max(-log10(pValToPlot))+0.2 |
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227 |
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228 if(length(significativePoints)>0){ |
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229 dataSignifToPlot=data.frame(pval=-log10(pValToPlot[significativePoints]),FC=coeffToPlot[significativePoints],description=paste(names(coeffToPlot[significativePoints]),"\n","FC: " , round(2^coeffToPlot[significativePoints],2) , " | Adjusted p-val: ",prettyNum(fdrToPlot[significativePoints],digits=4), sep="")) |
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230 #to test if remains any normal points to draw |
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231 if(length(significativePoints)<length(pValToPlot)){ |
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232 dataToPlot=data.frame(pval=-log10(pValToPlot[-significativePoints]),FC=coeffToPlot[-significativePoints],description=paste("FC: " , round(2^coeffToPlot[-significativePoints],2) , " | Adjusted p-val: ",prettyNum(fdrToPlot[-significativePoints],digits=4), sep="")) |
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233 }else{ |
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234 dataToPlot=data.frame(pval=0,FC=0,description="null") |
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235 } |
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236 }else{ |
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237 dataToPlot=data.frame(pval=-log10(pValToPlot),FC=coeffToPlot,description=paste("FC: " , round(2^coeffToPlot,2) , " | Adjusted p-val: ",prettyNum(fdrToPlot,digits=4), sep="")) |
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238 } |
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239 |
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240 ##traditional plot |
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241 |
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242 p <- ggplot(data=dataToPlot, aes(x=FC, y=pval)) + geom_point() + |
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243 theme_bw() + ggtitle(curentVolcanoName) + ylab(label="-Log10(p-val)") + xlab(label="Log2 Fold Change") + |
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244 theme(panel.border=element_blank(),plot.title = element_text(hjust = 0.5),legend.position="none") |
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245 if(logFCthreshold!=0) p <- p + geom_vline(xintercept=-logFCthreshold, color="salmon",linetype="dotted", size=1) + geom_vline(xintercept=logFCthreshold, color="salmon",linetype="dotted", size=1) + geom_text(data.frame(text=c(paste(c("log2(1/FC=",opt$fcThreshold,")"),collapse=""),paste(c("log2(FC=",opt$fcThreshold,")"),collapse="")),x=c(-logFCthreshold,logFCthreshold),y=c(0,0)),mapping=aes(x=x, y=y, label=text), size=4, angle=90, vjust=-0.4, hjust=0, color="salmon") |
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246 if(!is.null(pvalThresholdFDR)) p <- p + geom_hline(yintercept=pvalThresholdFDR, color="skyblue1",linetype="dotted", size=0.5) + geom_text(data.frame(text=c(paste(c("Adjusted pval limit(",opt$fdrThreshold,")"),collapse="")),x=c(xMinLimPlot),y=c(pvalThresholdFDR)),mapping=aes(x=x, y=y, label=text), size=4, vjust=0, hjust=0, color="skyblue3") |
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247 if(length(significativePoints)>0)p <- p + geom_point(data=dataSignifToPlot,aes(colour=description)) |
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248 |
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249 ##interactive plot |
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250 |
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251 if(length(htmlPointsToRemove)>0){ |
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252 pointToRemove=union(htmlPointsToRemove,significativePoints) |
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253 #to test if it remains any normal points to draw |
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254 if(length(pointToRemove)<length(pValToPlot)){ |
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255 dataToPlot=data.frame(pval=-log10(pValToPlot[-pointToRemove]),FC=coeffToPlot[-pointToRemove],description=paste("FC: " , round(2^coeffToPlot[-pointToRemove],2) , " | Adjusted p-val: ", prettyNum(fdrToPlot[-pointToRemove],digits=4), sep="")) |
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256 }else{ |
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257 dataToPlot=data.frame(pval=0,FC=0,description="null") |
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258 } |
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259 } |
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260 |
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261 if((nrow(dataToPlot)+length(significativePoints))>40000)addComment(c("[WARNING]For",curentVolcanoName,"volcano, numerous points to plot(",nrow(dataToPlot)+nrow(dataSignifToPlot),"), resulting volcano could be heavy, using more stringent thresholds could be helpful."),T,opt$log) |
14045c80a222
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262 |
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263 phtml <- plot_ly(data=dataToPlot, x=~FC, y=~pval,type="scatter", mode="markers",showlegend = FALSE, marker = list(color="gray",opacity=0.5), text=~description, hoverinfo="text") %>% |
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264 layout(title = curentVolcanoName[iVolcano],xaxis=list(title="Log2 Fold Change",showgrid=TRUE, zeroline=FALSE),yaxis=list(title="-Log10(p-val)", showgrid=TRUE, zeroline=FALSE)) |
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265 if(length(significativePoints)>0) phtml=add_markers(phtml,data=dataSignifToPlot, x=~FC, y=~pval, mode="markers" , marker=list( color=log10(abs(dataSignifToPlot$FC)*dataSignifToPlot$pval),colorscale='Rainbow'), text=~description, hoverinfo="text", inherit = FALSE) %>% hide_colorbar() |
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266 if(logFCthreshold!=0){ |
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267 phtml=add_trace(phtml,x=c(-logFCthreshold,-logFCthreshold), y=c(0,yMaxLimPlot), type="scatter", mode = "lines", line=list(color="coral",dash="dash"), hoverinfo='none', showlegend = FALSE,inherit = FALSE) |
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268 phtml=add_annotations(phtml,x=-logFCthreshold,y=0,xref = "x",yref = "y",text = paste(c("log2(1/FC=",opt$fcThreshold,")"),collapse=""),xanchor = 'right',showarrow = F,textangle=270,font=list(color="coral")) |
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269 phtml=add_trace(phtml,x=c(logFCthreshold,logFCthreshold), y=c(0, yMaxLimPlot), type="scatter", mode = "lines", line=list(color="coral",dash="dash"), hoverinfo='none', showlegend = FALSE,inherit = FALSE) |
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270 phtml=add_annotations(phtml,x=logFCthreshold,y=0,xref = "x",yref = "y",text = paste(c("log2(FC=",opt$fcThreshold,")"),collapse=""),xanchor = 'right',showarrow = F,textangle=270,font=list(color="coral")) |
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271 } |
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272 if(!is.null(pvalThresholdFDR)){ |
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273 phtml=add_trace(phtml,x=c(xMinLimPlot,xMaxLimPlot), y=c(pvalThresholdFDR,pvalThresholdFDR), type="scatter", mode = "lines", line=list(color="cornflowerblue",dash="dash"), hoverinfo='none', showlegend = FALSE,inherit = FALSE) |
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274 phtml=add_annotations(phtml,x=xMinLimPlot,y=pvalThresholdFDR+0.1,xref = "x",yref = "y",text = paste(c("Adjusted pval limit(",opt$fdrThreshold,")"),collapse=""),xanchor = 'left',showarrow = F,font=list(color="cornflowerblue")) |
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275 } |
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276 plotVector[[length(plotVector)+1]]=p |
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277 |
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278 #save plotly files |
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279 pp <- ggplotly(phtml) |
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280 htmlwidgets::saveWidget(as_widget(pp), paste(c(file.path(getwd(), "plotLyDir"),"/Volcanos_",volcanoFileName,".html"),collapse=""),selfcontained = F) |
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281 |
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282 |
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283 if(iVolcano==nbVolcanosToPlot || length(plotVector)==volcanoPerPage){ |
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284 #plot and close the actual plot |
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285 if(opt$format=="pdf"){ |
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286 pdf(paste(c("./plotDir/Volcanos_",volcanoFileName,".pdf"),collapse=""))}else{ |
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287 png(paste(c("./plotDir/Volcanos_",volcanoFileName,".png"),collapse="")) |
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288 } |
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289 multiplot(plotlist=plotVector,cols=1) |
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290 dev.off() |
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291 if(iVolcano<nbVolcanosToPlot){ |
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292 #prepare for a new ploting file if necessary |
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293 plotVector=list() |
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294 iToPlot=iToPlot+1 |
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295 } |
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296 } |
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297 } |
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298 remove(dataToPlot,dataSignifToPlot) |
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299 addComment("[INFO]Volcanos drawn",T,opt$log,T,display=FALSE) |
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300 |
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301 |
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302 #now add anotation infos about genes |
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303 |
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304 rowItemInfo=NULL |
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305 if(!is.null(opt$rowNameType) && !is.null(opt$organismID)){ |
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306 ##get gene information from BioMart |
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307 #if(!require("biomaRt")){ |
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308 # source("https://bioconductor.org/biocLite.R") |
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309 # biocLite("biomaRt") |
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310 #} |
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311 |
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312 ensembl_hs_mart <- useMart(biomart="ensembl", dataset=opt$organismID) |
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313 ensembl_df <- getBM(attributes=c(opt$rowNameType,"description"),mart=ensembl_hs_mart) |
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314 rowItemInfo=ensembl_df[which(ensembl_df[,1]!=""),2] |
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315 rowItemInfo=unlist(lapply(rowItemInfo,function(x)substr(unlist(strsplit(x," \\[Source"))[1],1,30))) |
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316 names(rowItemInfo)=ensembl_df[which(ensembl_df[,1]!=""),1] |
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317 } |
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318 |
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319 #filter out genes with higher p-values for all comparisons |
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320 genesToKeep=names(which(apply(dataFrame$adj_p.value,1,function(x)length(which(x<=opt$fdrThreshold))>0))) |
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321 #filter out genes with lower FC for all comparisons |
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322 genesToKeep=intersect(genesToKeep,names(which(apply(dataFrame$coefficients,1,function(x)length(which(abs(x)>=logFCthreshold))>0)))) |
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323 |
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324 if(length(genesToKeep)>0){ |
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325 dataFrameNew=data.frame(row.names=genesToKeep) |
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326 |
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327 dataFrameNew$adj_p.value=matrix(dataFrame$adj_p.value[genesToKeep,,drop=FALSE],ncol=ncol(dataFrame$adj_p.value)) |
14045c80a222
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328 rownames(dataFrameNew$adj_p.value)=genesToKeep |
14045c80a222
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329 colnames(dataFrameNew$adj_p.value)=colnames(dataFrame$p.value) |
14045c80a222
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330 |
14045c80a222
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331 dataFrameNew$p.value=matrix(dataFrame$p.value[genesToKeep,,drop=FALSE],ncol=ncol(dataFrame$p.value)) |
14045c80a222
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332 rownames(dataFrameNew$p.value)=genesToKeep |
14045c80a222
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vandelj
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333 colnames(dataFrameNew$p.value)=colnames(dataFrame$adj_p.value) |
14045c80a222
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334 |
14045c80a222
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335 dataFrameNew$coefficients=matrix(dataFrame$coefficients[genesToKeep,,drop=FALSE],ncol=ncol(dataFrame$coefficients)) |
14045c80a222
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336 rownames(dataFrameNew$coefficients)=genesToKeep |
14045c80a222
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vandelj
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337 colnames(dataFrameNew$coefficients)=colnames(dataFrame$adj_p.value) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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338 |
14045c80a222
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vandelj
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339 dataFrame=dataFrameNew |
14045c80a222
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vandelj
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340 rm(dataFrameNew) |
14045c80a222
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vandelj
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341 }else{ |
14045c80a222
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vandelj
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342 addComment("[WARNING]No significative genes",T,opt$log,display=FALSE) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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343 } |
14045c80a222
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344 |
14045c80a222
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vandelj
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345 addComment("[INFO]Significant genes filtering done",T,opt$log,T,display=FALSE) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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346 |
14045c80a222
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347 |
14045c80a222
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348 #plot VennDiagramm for genes below threshold between comparisons |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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349 #t=apply(dataFrame$adj_p.value[,1:4],2,function(x)names(which(x<=opt$threshold))) |
14045c80a222
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vandelj
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350 #get.venn.partitions(t) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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351 #vennCounts(dataFrame$adj_p.value[,1:4]<=opt$threshold) |
14045c80a222
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352 |
14045c80a222
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vandelj
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353 #make a simple sort genes based only on the first comparison |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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354 #newOrder=order(dataFrame$adj_p.value[,1]) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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355 #dataFrame$adj_p.value=dataFrame$adj_p.value[newOrder,] |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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356 |
14045c80a222
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vandelj
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357 #alternative sorting strategy based on the mean gene rank over all comparisons |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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358 if(length(genesToKeep)>1){ |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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359 currentRank=rep(0,nrow(dataFrame$adj_p.value)) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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360 for(iVolcano in 1:ncol(dataFrame$adj_p.value)){ |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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361 currentRank=currentRank+rank(dataFrame$adj_p.value[,iVolcano]) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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362 } |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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363 currentRank=currentRank/ncol(dataFrame$adj_p.value) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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364 newOrder=order(currentRank) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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365 rownames(dataFrame)=rownames(dataFrame)[newOrder] |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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366 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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367 dataFrame$adj_p.value=matrix(dataFrame$adj_p.value[newOrder,],ncol=ncol(dataFrame$adj_p.value)) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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368 rownames(dataFrame$adj_p.value)=rownames(dataFrame$p.value)[newOrder] |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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369 colnames(dataFrame$adj_p.value)=colnames(dataFrame$p.value) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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370 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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371 dataFrame$p.value=matrix(dataFrame$p.value[newOrder,],ncol=ncol(dataFrame$p.value)) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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372 rownames(dataFrame$p.value)=rownames(dataFrame$adj_p.value) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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373 colnames(dataFrame$p.value)=colnames(dataFrame$adj_p.value) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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374 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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375 dataFrame$coefficients=matrix(dataFrame$coefficients[newOrder,],ncol=ncol(dataFrame$coefficients)) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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376 rownames(dataFrame$coefficients)=rownames(dataFrame$adj_p.value) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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377 colnames(dataFrame$coefficients)=colnames(dataFrame$adj_p.value) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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378 } |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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379 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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380 #formating output matrix depending on genes to keep |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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381 if(length(genesToKeep)==0){ |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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382 outputData=matrix(0,ncol=ncol(dataFrame$adj_p.value)*4+2,nrow=3) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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383 outputData[1,]=c("X","X",rep(volcanoNameList,each=4)) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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384 outputData[2,]=c("X","X",rep(c("p-val","Adjusted.p-val","FC","log2(FC)"),ncol(dataFrame$adj_p.value))) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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385 outputData[,1]=c("Volcano","Gene","noGene") |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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386 outputData[,2]=c("Comparison","Info","noInfo") |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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387 }else{ |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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388 if(length(genesToKeep)==1){ |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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389 outputData=matrix(0,ncol=ncol(dataFrame$adj_p.value)*4+2,nrow=3) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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390 outputData[1,]=c("X","X",rep(volcanoNameList,each=4)) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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391 outputData[2,]=c("X","X",rep(c("p-val","Adjusted.p-val","FC","log2(FC)"),ncol(dataFrame$adj_p.value))) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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392 outputData[,1]=c("Volcano","Gene",genesToKeep) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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393 outputData[,2]=c("Comparison","Info","na") |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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394 if(!is.null(rowItemInfo))outputData[3,2]=rowItemInfo[genesToKeep] |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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395 outputData[3,seq(3,ncol(outputData),4)]=prettyNum(dataFrame$p.value,digits=4) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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396 outputData[3,seq(4,ncol(outputData),4)]=prettyNum(dataFrame$adj_p.value,digits=4) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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397 outputData[3,seq(5,ncol(outputData),4)]=prettyNum(2^dataFrame$coefficients,digits=4) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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398 outputData[3,seq(6,ncol(outputData),4)]=prettyNum(dataFrame$coefficients,digits=4) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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399 }else{ |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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400 #format matrix to be correctly read by galaxy (move headers in first column and row) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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401 outputData=matrix(0,ncol=ncol(dataFrame$adj_p.value)*4+2,nrow=nrow(dataFrame$adj_p.value)+2) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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402 outputData[1,]=c("X","X",rep(volcanoNameList,each=4)) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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403 outputData[2,]=c("X","X",rep(c("p-val","Adjusted.p-val","FC","log2(FC)"),ncol(dataFrame$adj_p.value))) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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404 outputData[,1]=c("Volcano","Gene",rownames(dataFrame$adj_p.value)) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
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405 outputData[,2]=c("Comparison","Info",rep("na",nrow(dataFrame$adj_p.value))) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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changeset
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406 if(!is.null(rowItemInfo))outputData[3:nrow(outputData),2]=rowItemInfo[rownames(dataFrame$adj_p.value)] |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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407 outputData[3:nrow(outputData),seq(3,ncol(outputData),4)]=prettyNum(dataFrame$p.value,digits=4) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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408 outputData[3:nrow(outputData),seq(4,ncol(outputData),4)]=prettyNum(dataFrame$adj_p.value,digits=4) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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409 outputData[3:nrow(outputData),seq(5,ncol(outputData),4)]=prettyNum(2^dataFrame$coefficients,digits=4) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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410 outputData[3:nrow(outputData),seq(6,ncol(outputData),4)]=prettyNum(dataFrame$coefficients,digits=4) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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411 } |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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412 } |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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413 addComment("[INFO]Formated output",T,opt$log,display=FALSE) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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414 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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415 #write output results |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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416 write.table(outputData,file=opt$outputFile,quote=FALSE,sep="\t",col.names = F,row.names = F) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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417 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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418 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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419 end.time <- Sys.time() |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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420 addComment(c("[INFO]Total execution time for R script:",as.numeric(end.time - start.time,units="mins"),"mins"),T,opt$log,display=FALSE) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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421 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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422 addComment("[INFO]End of R script",T,opt$log,display=FALSE) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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423 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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424 printSessionInfo(opt$log) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
425 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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426 #sessionInfo() |